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Nelfe negative elongation factor complex member E [ Rattus norvegicus (Norway rat) ]

Gene ID: 294258, updated on 17-Aug-2024

Summary

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Official Symbol
Nelfeprovided by RGD
Official Full Name
negative elongation factor complex member Eprovided by RGD
Primary source
RGD:1303325
See related
EnsemblRapid:ENSRNOG00000000420 AllianceGenome:RGD:1303325
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Rd; Rdbp
Summary
Enables chromatin binding activity. Involved in positive regulation of ERK1 and ERK2 cascade; positive regulation of histone H3-K4 methylation; and regulation of transcription by RNA polymerase II. Located in nucleus. Orthologous to human NELFE (negative elongation factor complex member E). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Adrenal (RPKM 120.8), Testes (RPKM 105.9) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
20p12
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3981259..3987016, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3976512..3982389, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4530328..4536085)

Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene zinc finger and BTB domain containing 12 Neighboring gene complement C2 Neighboring gene complement factor B Neighboring gene SKI2 subunit of superkiller complex Neighboring gene decapping exoribonuclease

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Striatal NELF-mediated RNA polymerase II stalling controls L-dopa induced dyskinesia. Bastide MF, et al. Neurobiol Dis, 2016 Jan. PMID 26480869
  2. Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II. Saha RN, et al. Nat Neurosci, 2011 May 29. PMID 21623364, Free PMC Article
  3. Negative elongation factor NELF controls transcription of immediate early genes in a stimulus-specific manner. Fujita T, et al. Exp Cell Res, 2009 Jan 15. PMID 19014935
  4. Transcription elongation factors are involved in programming hormone production in pituitary neuroendocrine GH4C1 cells. Fujita T, et al. Mol Cell Endocrinol, 2010 May 5. PMID 20097260
  5. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Flynn RA, et al. Proc Natl Acad Sci U S A, 2011 Jun 28. PMID 21670248, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NELF-mediated RNA polymerase II stalling plays a key role in L-Dopa-induced dyskinesia pathophysiology
    Title: Striatal NELF-mediated RNA polymerase II stalling controls L-dopa induced dyskinesia.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables RNA binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables mRNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription elongation by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within negative regulation of transcription elongation by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of transcription elongation by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of ERK1 and ERK2 cascade IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein modification process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of NELF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of NELF complex ISO
Inferred from Sequence Orthology
more info
  
part_of chromatin ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear body IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear body ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
negative elongation factor E
Names
RD RNA-binding protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001165901.1 → NP_001159373.1  negative elongation factor E

    See identical proteins and their annotated locations for NP_001159373.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC079427, CO401737
    UniProtKB/TrEMBL
    A0A8J8XR86, F1LP40, Q6AXP2, Q6MG75
    Related
    ENSRNOP00000000478.6, ENSRNOT00000000478.9
    Conserved Domains (1) summary
    cd12305
    Location:256 → 330
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

  2. NM_212548.2 → NP_997713.1  negative elongation factor E

    See identical proteins and their annotated locations for NP_997713.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC079427
    UniProtKB/TrEMBL
    A0A8J8XR86, F1LP40, Q6AXP2, Q6MG75
    Related
    ENSRNOP00000098069.1, ENSRNOT00000120387.2
    Conserved Domains (1) summary
    cd12305
    Location:256 → 330
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086038.1 Reference GRCr8

    Range
    3981259..3987016 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006255922.5 → XP_006255984.1  negative elongation factor E isoform X1

    See identical proteins and their annotated locations for XP_006255984.1

    UniProtKB/TrEMBL
    A0A8J8XR86, F1LP40, Q6AXP2, Q6MG75
    Conserved Domains (1) summary
    cd12305
    Location:256 → 330
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins
Nucleotide Protein Strain
Heading Accession and Version

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